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- PDB-1qaj: CRYSTAL STRUCTURES OF THE N-TERMINAL FRAGMENT FROM MOLONEY MURINE... -

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Basic information

Entry
Database: PDB / ID: 1qaj
TitleCRYSTAL STRUCTURES OF THE N-TERMINAL FRAGMENT FROM MOLONEY MURINE LEUKEMIA VIRUS REVERSE TRANSCRIPTASE COMPLEXED WITH NUCLEIC ACID: FUNCTIONAL IMPLICATIONS FOR TEMPLATE-PRIMER BINDING TO THE FINGERS DOMAIN
Components
  • DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')
  • REVERSE TRANSCRIPTASE
KeywordsTRANSFERASE/DNA / PROTEIN-DNA COMPLEX / POLYMERASE / REVERSE TRANSCRIPTASE / MOLONEY MURINE LEUKEMIA VIRUS / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / virion assembly / protein-DNA complex / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / virion assembly / protein-DNA complex / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / structural constituent of virion / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein ...Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / : / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsNajmudin, S. / Cote, M. / Sun, D. / Yohannan, S. / Montano, S.P. / Gu, J. / Georgiadis, M.M.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structures of an N-terminal fragment from Moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain.
Authors: Najmudin, S. / Cote, M.L. / Sun, D. / Yohannan, S. / Montano, S.P. / Gu, J. / Georgiadis, M.M.
#1: Journal: Protein Sci. / Year: 1998
Title: Cloning, expression and purification of a catalytic fragment of Moloney murine leukemia virus reverse transcriptase: Crystallization of nucleic acid complexes
Authors: Sun, D. / Jessen, S. / Liu, C. / Liu, X. / Najmudin, S. / Georgiadis, M.
History
DepositionMar 18, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')
D: DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')
A: REVERSE TRANSCRIPTASE
B: REVERSE TRANSCRIPTASE


Theoretical massNumber of molelcules
Total (without water)63,5494
Polymers63,5494
Non-polymers00
Water7,314406
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.868, 63.587, 73.398
Angle α, β, γ (deg.)90.00, 102.91, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: DNA chain DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')


Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein REVERSE TRANSCRIPTASE / E.C.2.7.7.49 / RT


Mass: 29347.754 Da / Num. of mol.: 2
Fragment: N-TERMINAL FRAGMENT COMPRISING FINGERS AND PALM DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus / Genus: Gammaretrovirus / Species: Murine leukemia virus / Gene: MMLV-RT / Plasmid: PRT 107-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P03355, RNA-directed DNA polymerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 4000, 0.1 M NH4CL,0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1NH4CL11
2HEPES11
3PEG 400011
4PEG 400012
Crystal grow
*PLUS
Details: Sun, D., (1998) Protein Sci., 7, 1575.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMHEPES1reservoir
213 %PEG40001reservoir
375 mM1reservoirNH4Cl
41

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 26120 / Num. obs: 26120 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 21.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.174 / % possible all: 97.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 91393
Reflection shell
*PLUS
Lowest resolution: 2.34 Å / % possible obs: 97.1 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1322 5 %RANDOM
Rwork0.2 ---
obs0.2 26120 98.7 %-
all-26120 --
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4128 322 0 406 4856
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.64
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.14
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.92

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